Input files

Files
  • Contig FASTA GJJD01.1.fsa_nt
  • Read1 FASTQ SRR15058678_1.fastq
  • Flagstat hisat2_SRR15058678.sort.flagstat.txt
  • Split srs_SRR15058678_split_alignments.txt
  • Candidat srs_SRR15058678_candidates.txt

Contigs

Contigs statistics
Contig FASTA - Number of sequences98 794
Contig FASTA - Mean sequence length827

Reads

Reads statistics
Number of reads10 490 833
Mean coverage12.92
Min reads length15
Max reads length101
Mean reads length100.59
Reads length distribution

Mapping (QC-passed reads)

Number of reads0
Number of lines in the BAM10 526 093
Number of mapped reads7 487 218
Percentage of mapped reads71.37
Number of properly paired reads0
Percentage of properly paired reads0
Secondary alignments35 260
Singletons alignements0

Intron extraction results

Split reads
Number of reads overlapping introns16 752
Mean length of introns270.64
Junction TC_GG927
Junction NN_NN702
Junction CT_GC405
Junction AT_AC339
Junction CT_NN242
Other junctions4 462
Canonical junction (GT_AG or CT_AC)9 675
Detected introns
Number3 191
Min length20
Max length5 511
Mean length223.01
Min depth1
Max depth2 376
Mean depth5.25
Detected introns depth distribution
Filtered detected introns
Number110
Filtered because of depth (<= 1)2 776
Filtered because of length (>= 80%)52
Filtered because of non canonical junction1 889
Filtered because of overlapping introns0
Min length21
Max length2 883
Mean length392.21
Min depth2
Max depth2 376
Mean depth46.5
Top 10 of contigs with the highest number of detected introns
GJJD01002985.12 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01085655.12 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000026.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000401.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000437.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000474.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01000541.11 PASS; 2 DP; 0 IO; 0 SS; 0 LEN
GJJD01002305.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01002766.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN
GJJD01003126.11 PASS; 0 DP; 0 IO; 0 SS; 0 LEN

Glossary

This glossary reflects terms used in this report:
Candidat : Detected/predicted introns filtrered by canonical junction, length and depth.
Canonic junction: GT_AG or CT_AC for donor and acceptor sites.
Contig : A set of overlapping DNA segments that together represent a consensus region of DNA (source :Wikipedia)
Exon : Coding part of DNA that is translated into protein.
Features : A sequenced chain of nucleic acids which provide protein(s). (source:https://biologydictionary.net/gene/)
Fragment : During sequencing, the fragment is a link between fowarded and reverse reads.
Intron : Any nucleotide sequence removed by RNA splicing during maturation of RNA. (source : Wikipedia)
Reads : An inferred sequence of base pairs corresponding to all or part of a single DNA fragment. (source : Wikipedia)
Sequence : Base pair probabilities of a DNA fragment.
Splice events : a process where exons may be included within or excluded from the final mRNA.
Trimmed contig : Contig without retained intron(s).

intronSeeker glossary